[phenixbb] phenix.real_space_refine

[Pavel Afonine]

On 10/24/16 23:50, Pavel Afonine wrote:
> I think "weight=1" may be a troublemaker.. It may be too far from 
> what's optimal (that program determines by default if you don't 
> specify any weight) and that may result in clashes that happen during 
> refinement. Of course, something else may cause this as well.
>
> Pavel
>
> On 10/24/16 20:07, Oleg Sobolev wrote:
>> Hi Julia,
>>
>> In addition to Dorothee's response to your another e-mail, I would 
>> indeed recommend check the model geometry, in particular, bad atomic 
>> clashes (where 2 atoms are very close to each other). You can find 
>> them in the .geo file which should be created by this point or in 
>> log, under "Nonbonded interactions:". The worst clashes will be the 
>> first in the list.
>>
>> Best regards,
>> Oleg Sobolev.
>>
>> On Mon, Oct 24, 2016 at 3:19 AM, Flis, Julia <julia.flis at charite.de 
>> <mailto:julia.flis at charite.de>> wrote:
>>
>>     Hello,
>>
>>     my question is about the Phenix real space refinement. I am using
>>     the Phenix version phenix-1.11-2563.
>>
>>     My command looks as follows:
>>     phenix.real_space_refine secondary_structure.enable=true
>>     Model.pdb VOL.map elbow.Model_pdb.001.cif Model.pdb_ss.eff
>>     resolution=3.8 weight=1
>>
>>     My problem is that the refinement suddenly stops during the first
>>     refinement cycle:
>>
>>
>>
>>     Model_real_space_refined.log says:
>>
>>     ********************** REFINEMENT MACRO_CYCLE 1 OF 5
>>     *************************
>>     -------------------------------------------------------------------------------
>>     Update NCS operators
>>     ********************
>>     -------------------------------------------------------------------------------
>>     Update rotamer restraints
>>     *************************
>>     -------------------------------------------------------------------------------
>>     Global refinement
>>     *****************
>>     END
>>
>>
>>     In the shell I get this :
>>
>>     [...]
>>       distance: 184426 - 184921:   3.388
>>       distance: 184428 - 184920:   3.342
>>       distance: 184448 - 184898:   3.373
>>       distance: 184449 - 184897:   3.187
>>       distance: 184491 - 184860:   3.066
>>       distance: 184531 - 184770:   3.203
>>       distance: 184554 - 184746:   3.137
>>
>>     then it stops and the only files generated are
>>     Model_real_space_refined.log and Model_initial.geo.
>>
>>     Could you give me an advise? I have no clue what the problem
>>     could be.
>>
>>     Thank you,
>>
>>     Julia
>>
>>
>

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